Tripal Developer's Meeting 2015-06-02

Meeting Date
Attendees

Stephen Ficklin, Connor Wytko, Brian Soto!, Sook, Jung, Taein Lee, Chun-Huai Cheng (WSU)
Andrew Farmer (NCGR)
Lacey Sanderson (U of Sask)
Sudhansu Dash (NCGR)
Nathan Henry (U Tennessee)
Gerard Lazo (ARS Albany, CA)
Valentin Guignon (Bioversity International)
Nathan Weeks (USDA-ARS)
Steven Cannon (USDA-ARS)
Ethy Cannon (ISU)
Chris Childers, Vijaya Tsvatapalli (USDA-ARS-NAL)

  • Tripal v2.0 stable release:  released June 1st!

  • Overview/Progress of changes since last meeting

    • Admin pages are faster.

      • Forms don’t perform search (show data) unless submitted

      • Drop-downs populated with loose index scan (patch supplied by Nathan).

      • Feature admin page has d3 bar graph summary of features.

        • We want user input on this feature before adding it to all of the admin pages.

        • Lacey will explore making this bar graph available for anonymous viewers.

    • URL setting will have a ‘type’ filter setting but it is not yet there.

    • Memory leaks have been fixed for removing orphaned features and syncing features..

    • Feature browser is now deprecated in v2.0, but is still available in the event someone is using it.  It will go away in some release in the future.

    • Add a drush command for syncing:  This didn’t make it in the v2.0 release but an issue was added. https://www.drupal.org/node/2498995

    • Chado v1.3 should have bigserial for the pkey fields to help with large tables.

      • There should be a Chado v1.3 release soon!

      • Tripal will be Chado v1.3 compatible shortly thereafter. A new Tripal release will be made at that point.

      • Ask Scott about the type_id on the organism table.

      • Andrew:  how to handle features associated at higher taxonomic ranks than genus.

      • Steve & Ethy: how to handle features at the genus level (or synthetic crosses). How to link featuremaps (currently using stocks for these). For featuremaps linked to stock record, and then linked the stock record to multiple stocks and those secondary stocks are linked to features. Create an organism record to represent multiple species.

        • Sook suggested:  markers are assigned to the organism from which the source DNA was extracted.  Then the marker feature can be associated with any maps even if organism doesn’t match.

        • Lacey:  for features that are for various species use ‘spp’ in species field of organism table.

  • Add / update your extensions on the tripal.info site.  http://tripal.info now supports logins.

  • Upcoming Changes / Features / Events

    • Phylogeny module release.

    • Other modules with upcoming releases?

    • Contemplating migration of Tripal to GitHub for improved code sharing and forking

      • A synced copy of the code will continue to remain on Drupal.org

      • Drupal.org will continue to provide releases.

      • Possibility of splitting the core Tripal modules into separate packages for easier code sharing (e.g. phylogeny module).

    • Web services design meeting.

  • Needs?

    • Valentin:  Is there a way to remove (or replace) data that was added via the bulk loader. For instance, for the stock_cvterm table. I have a stock linked to the cvterm ‘in vitro collection’ (through stock_cvterm table) and I’d like to have it linked (during an update job) to the cvterm ‘cryo-preserved’ instead. It means either removing previous relationship and adding the new one or updating the stock_cvterm.cvterm_id. Those 2 terms belong to the same CV but other terms from that CV might be used for current stock and should not be removed.

    • Andrew:  Need a public accessible way to view terms with information about parental terms (tree to show relationships).

    • Sook/Jing:  How to add bulk load publication that are not available in PubMed or Agricola.   How about a bibtex loader?  Lacey may make a bulk loader template. Will add an issue to the Tripal issue queue.  

      • Steve Cannon:  EndNote exports to flat files and a perl script is used to load those pubs.  Will be happy to share that script.  Can post on Tripal.info site:  1) Documentation for how to dump from EndNote and convert to flat file.  2) Use perl loader to import.

      • Valentin:  how can we integrate with the Drupal biblio module.

  • Items from last meeting agenda that were not discussed

    • Downloads: it would be nice to have downloads built in to Tripal, especially downloads of search results, configurable as to which fields from the record pages to include. In the meantime, what have other groups done? (EC) NB: this relates to an issue I raised for our site regarding the views-data-export module listed as a "Highly Recommended Module" in the README that comes with tripal (ADF)

      • Lacey uses the Drupal module views_data_export.  But she’s not very happy. It can be very slow and doesn’t clean up interrupted downloads.

      • Stephen: will add an issue to the Tripal issue queue.  Update the documentation to indicate the issues with the views_data_export.

    • Permissions: having to manually reset permissions for modules on install seems to trip us up frequently during development/deployment. Is there a reason that modules should not have some default permission settings and if not, is there a way to effect this? (ADF)

      • Lacey: setting permission by default may make security assumptions not desired by others.

        • Should we set ‘view’ permissions by default for authenticated users?

      • Chun-huai:  add a global setting to set default module permissions.

        • Stephen: will add an issue to explore this option.

      • Andrew other site-specific settings… a topic to discuss for more use cases….  Stephen: add an issue so we don’t forget it.

  • Any other items?

    • Sudhansu: Help/user-guide feature for modules (e.g., Phylotree module). Need a way to provide help for users.  Is working on a module(a generic include file for now) for adding ‘Help’ tabs to each content type page.  The inc file creates a small block at the top of a target page with a short message and an optional link to a more detailed help page. The detailed help page is included as an html file in the module dir. So, the code is not dispersed and stays with the module for portability.

      • Lacey: Drupal working towards interactive site tours.  She is creating this for knowpulse.  The tools is a JavaScript library called Shepherd.  Another javascript library is Joyride but Lacey feels it wasn’t as accurate as highlighting the exact element she wanted.

      • http://github.hubspot.com/shepherd/docs/welcome/ shows an example (obviously color is configurable :) )

      • Stephen:  Can use collapsible fieldset that contains the help text.

      • Maybe meet later in July - August for a separate meeting on help.

  • Next meeting July 7th.

  • Action Items:

https://www.drupal.org/node/2499881

Meeting Type
Users